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==Crystal structure of metal-dependent hydrolase ybeY from E. coli, Pfam UPF0054==
==Crystal structure of metal-dependent hydrolase ybeY from E. coli, Pfam UPF0054==
<StructureSection load='1xm5' size='340' side='right' caption='[[1xm5]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
<StructureSection load='1xm5' size='340' side='right'caption='[[1xm5]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1xm5]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XM5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XM5 FirstGlance]. <br>
<table><tr><td colspan='2'>[[1xm5]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XM5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XM5 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.7&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ybeY ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1xm5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xm5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xm5 RCSB], [http://www.ebi.ac.uk/pdbsum/1xm5 PDBsum], [http://www.topsan.org/Proteins/NYSGXRC/1xm5 TOPSAN]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1xm5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xm5 OCA], [https://pdbe.org/1xm5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xm5 RCSB], [https://www.ebi.ac.uk/pdbsum/1xm5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xm5 ProSAT], [https://www.topsan.org/Proteins/NYSGXRC/1xm5 TOPSAN]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/YBEY_ECOLI YBEY_ECOLI]] Single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA. Acts together with the RNase R to eliminate defective 70S ribosomes, but not properly matured 70S ribosomes or individual subunits, by a process mediated specifically by the 30S ribosomal subunit. Involved in the processing of 16S, 23S and 5S rRNAs, with a particularly strong effect on maturation at both the 5'-and 3'-ends of 16S rRNA as well as maturation of the 5'-end of 23S and 5S rRNAs.<ref>PMID:20639334</ref> <ref>PMID:20807199</ref> <ref>PMID:23273979</ref> <ref>PMID:16511207</ref>
[https://www.uniprot.org/uniprot/YBEY_ECOLI YBEY_ECOLI] Single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA. Acts together with the RNase R to eliminate defective 70S ribosomes, but not properly matured 70S ribosomes or individual subunits, by a process mediated specifically by the 30S ribosomal subunit. Involved in the processing of 16S, 23S and 5S rRNAs, with a particularly strong effect on maturation at both the 5'-and 3'-ends of 16S rRNA as well as maturation of the 5'-end of 23S and 5S rRNAs.<ref>PMID:20639334</ref> <ref>PMID:20807199</ref> <ref>PMID:23273979</ref> <ref>PMID:16511207</ref>  
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xm/1xm5_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xm/1xm5_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
   </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1xm5 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The three-dimensional crystallographic structure of the ybeY protein from Escherichia coli (SwissProt entry P77385) is reported at 2.7 A resolution. YbeY is a hypothetical protein that belongs to the UPF0054 family. The structure reveals that the protein binds a metal ion in a tetrahedral geometry. Three coordination sites are provided by histidine residues, while the fourth might be a water molecule that is not seen in the diffraction map because of its relatively low resolution. X-ray fluorescence analysis of the purified protein suggests that the metal is a nickel ion. The structure of ybeY and its sequence similarity to a number of predicted metal-dependent hydrolases provides a functional assignment for this protein family. The figures and tables of this paper were prepared using semi-automated tools, termed the Autopublish server, developed by the New York Structural GenomiX Research Consortium, with the goal of facilitating the rapid publication of crystallographic structures that emanate from worldwide Structural Genomics efforts, including the NIH-funded Protein Structure Initiative.
The ybeY protein from Escherichia coli is a metalloprotein.,Zhan C, Fedorov EV, Shi W, Ramagopal UA, Thirumuruhan R, Manjasetty BA, Almo SC, Fiser A, Chance MR, Fedorov AA Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005 Nov 1;61(Pt, 11):959-63. Epub 2005 Oct 20. PMID:16511207<ref>PMID:16511207</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
== References ==
== References ==
<references/>
<references/>
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</StructureSection>
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Almo, S C]]
[[Category: Large Structures]]
[[Category: Burley, S K]]
[[Category: Almo SC]]
[[Category: Fedorov, A A]]
[[Category: Burley SK]]
[[Category: Fedorov, E V]]
[[Category: Fedorov AA]]
[[Category: Structural genomic]]
[[Category: Fedorov EV]]
[[Category: Ramagopal, U A]]
[[Category: Ramagopal UA]]
[[Category: Shi, W]]
[[Category: Shi W]]
[[Category: Thirumuruhan, R]]
[[Category: Thirumuruhan R]]
[[Category: NYSGXRC, New York SGX Research Center for Structural Genomics]]
[[Category: Pfam family upf0054]]
[[Category: PSI, Protein structure initiative]]
[[Category: Unknown function]]

Latest revision as of 11:51, 14 February 2024

Crystal structure of metal-dependent hydrolase ybeY from E. coli, Pfam UPF0054Crystal structure of metal-dependent hydrolase ybeY from E. coli, Pfam UPF0054

Structural highlights

1xm5 is a 4 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.7Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

YBEY_ECOLI Single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA. Acts together with the RNase R to eliminate defective 70S ribosomes, but not properly matured 70S ribosomes or individual subunits, by a process mediated specifically by the 30S ribosomal subunit. Involved in the processing of 16S, 23S and 5S rRNAs, with a particularly strong effect on maturation at both the 5'-and 3'-ends of 16S rRNA as well as maturation of the 5'-end of 23S and 5S rRNAs.[1] [2] [3] [4]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

References

  1. ↑ Rasouly A, Davidovich C, Ron EZ. The heat shock protein YbeY is required for optimal activity of the 30S ribosomal subunit. J Bacteriol. 2010 Sep;192(18):4592-6. doi: 10.1128/JB.00448-10. Epub 2010 Jul 16. PMID:20639334 doi:http://dx.doi.org/10.1128/JB.00448-10
  2. ↑ Davies BW, Kohrer C, Jacob AI, Simmons LA, Zhu J, Aleman LM, Rajbhandary UL, Walker GC. Role of Escherichia coli YbeY, a highly conserved protein, in rRNA processing. Mol Microbiol. 2010 Oct;78(2):506-18. doi: 10.1111/j.1365-2958.2010.07351.x. Epub, 2010 Sep 16. PMID:20807199 doi:http://dx.doi.org/10.1111/j.1365-2958.2010.07351.x
  3. ↑ Jacob AI, Kohrer C, Davies BW, RajBhandary UL, Walker GC. Conserved bacterial RNase YbeY plays key roles in 70S ribosome quality control and 16S rRNA maturation. Mol Cell. 2013 Feb 7;49(3):427-38. doi: 10.1016/j.molcel.2012.11.025. Epub 2012, Dec 27. PMID:23273979 doi:http://dx.doi.org/10.1016/j.molcel.2012.11.025
  4. ↑ Zhan C, Fedorov EV, Shi W, Ramagopal UA, Thirumuruhan R, Manjasetty BA, Almo SC, Fiser A, Chance MR, Fedorov AA. The ybeY protein from Escherichia coli is a metalloprotein. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005 Nov 1;61(Pt, 11):959-63. Epub 2005 Oct 20. PMID:16511207 doi:10.1107/S1744309105031131

1xm5, resolution 2.70Å

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